Rank‐based characterization of pollen assemblages collected by honey bees using a multi‐locus metabarcoding approach

Richardson, Rodney T.; Lin, Chia‐Hua; Quijia, Juan O.; Riusech, Natalia S; Goodell, Karen; Johnson, Reed M.

doi:10.3732/apps.1500043

Cited by 114 publications

(146 citation statements)

References 29 publications

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“…As a first guideline, Sickel et al (2015) report 2000-3000 high-quality reads to be adequate to describe bee-collected samples with up to 80 taxa included. Lastly, pollen metabarcoding has been successfully conducted using a variety of platforms including Ion Torrent (Kraaijeveld et al 2015), Roche 454 (Valentini et al 2010;Hawkins et al 2015;Keller et al 2015), and Illumina (Richardson et al 2015a(Richardson et al , 2015bSickel et al 2015); however, with increased relative throughput, accurate homopolymer sequencing and increasing length capabilities, we see Illumina as the current platform of choice for PCR-based approaches.…”

Section: Component 4: Sequencing Methodologies and Bioinformatics Pipmentioning

confidence: 99%

“…The theoretically lower copy number of ptDNA could decrease amplification efficiency of ptDNA barcodes, although this has not been observed in practice (Valentini et al 2010;Galimberti et al 2014;Bruni et al 2015;Hawkins et al 2015;Kraaijeveld et al 2015;Richardson et al 2015a). While five different markers have been employed with relative success in pollen DNA metabarcoding, only data from rbcL, matK, ITS2, and trnL have been compared with microscopic palynology for assessment of qualitative and quantitative consistency, and further comparisons across a broader scope of taxa are needed.…”

Section: Component 2: Genetic Markersmentioning

confidence: 99%

“…The latter has mostly been superseded by HTS approaches for DNA metabarcoding. More recent HTSbased studies have employed one of three major sequencing library preparation strategies: ligation-based "tagmentation" kits (Richardson et al 2015a(Richardson et al , 2015b, singly indexed barcoded primers (Valentini et al 2010;Hawkins et al 2015;Keller et al 2015;Kraaijeveld et al 2015), or dual-indexed barcoded primers (Sickel et al 2015). The dual-indexing approach described in Sickel et al (2015), adapted from Kozich et al (2013), shows great promise for facilitating library preparation for large studies while reducing multiplexing cost and increasing laboratory efficiency.…”

Section: Component 4: Sequencing Methodologies and Bioinformatics Pipmentioning

confidence: 99%

“…Following similar observations, suggestions that plastid DNA (ptDNA) was absent from the pollen (e.g., Willerslev et al 2003) may have discouraged early development of pollen DNA barcoding methods. Several studies have now shown proof-of-concept for amplification of ptDNA from pollen (Galimberti et al 2014;Hawkins et al 2015;Kraaijeveld et al 2015;Richardson et al 2015a), so this is no longer considered an issue.…”

Section: Background and Potential Of Pollen Dna Barcodingmentioning

confidence: 99%

“…Further investigation is required to assess the potential for such enzymes in DNA extraction from pollen. For DNA extraction, studies to date have largely relied on proprietary kits including the QIAamp DNA Mini Kit (Kraaijeveld et al 2015), Qiagen DNeasy Plant Mini Kit (Galimberti et al 2014;Bruni et al 2015;Hawkins et al 2015;Richardson et al 2015aRichardson et al , 2015b, and Machery-Nagel NucleoSpin Food Kit Sickel et al 2015). It is, however, currently unclear to what extent different extraction strategies are comparable.…”

Section: Component 1: the Pollen Dna Templatementioning

confidence: 99%

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Pollen DNA barcoding: current applications and future prospects

Bell

Vere

Keller

et al. 2016

Genome

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205

170

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Identification of the species origin of pollen has many applications, including assessment of plant-pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.Key words: DNA metabarcoding, metagenomics, pollen, palynology, high-throughput sequencing, next-generation sequencing.Résumé : L'identification de l'espèce à l'origine d'un pollen se prête à de nombreuses applications dont la description des réseaux plante-pollinisateur, la reconstruction de communautés de plantes anciennes, l'authentification de produits, la surveillance des allergènes et les enquêtes médicolégales. Cependant, ces applications ont précédemment été limitées à l'identification du pollen par examen microscopique, un processus lent, à faible résolution taxonomique et qui compte peu de praticiens experts. Une alternative est l'identification du pollen par le recours aux codes à barres de l'ADN, une avenue qui permettrait de surmonter plusieurs de ces limitations. De récentes études ont montré qu'il était possible d'amplifier les marqueurs de codage tant chloroplastiques que nucléaires à partir du pollen. Ces récentes validations du métacodage à barres chez le pollen indiquent qu'il est maintenant opportun pour les chercheurs dans divers domaines de considérer l'emploi de ces méthodes dans leurs programmes de recherche. Dans cet article, les auteurs passent en revue le domaine naissant du codage à barres du pollen et discutent des nouvelles applications potentielles de cette technologie en mettant en lumière les limitations existantes ainsi que de futurs développements qui pourraient accroître son utilité dans un grand nombre d'applications. [Traduit par la Rédaction] Mots-clés : métacodage à barres, métagénomique, pollen, palynologie, séquençage à haut débit, séquençage de nouvelle génération.

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Section: Component 4: Sequencing Methodologies and Bioinformatics Pipmentioning

confidence: 99%

Section: Component 2: Genetic Markersmentioning

confidence: 99%

Section: Component 4: Sequencing Methodologies and Bioinformatics Pipmentioning

confidence: 99%

Section: Background and Potential Of Pollen Dna Barcodingmentioning

confidence: 99%

Section: Component 1: the Pollen Dna Templatementioning

confidence: 99%

See 3 more Smart Citations

Pollen DNA barcoding: current applications and future prospects

Bell

Vere

Keller

et al. 2016

Genome

Self Cite

205

170

View full text Add to dashboard Cite

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Monitoring of honey bee floral resources with pollen DNA metabarcoding as a complementary tool to vegetation surveys

Milla

Schmidt‐Lebuhn

Bovill

et al. 2022

Ecol Sol and Evidence

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Monitoring biodiversity is a growing and pressing challenge, particularly as climate change threatens species with extinction and leads to widespread shifts in plant distribution and phenology. Tracking changes via ground vegetation surveys is costly and time‐consuming, hence monitoring of complex and heterogenous communities remains an ongoing challenge. Molecular DNA methods are rapidly being developed to provide fast and reproducible results for environmental monitoring, including diet and ecosystem assessments. Here, we used DNA metabarcoding of pollen foraged by European honey bees (Apis mellifera) to investigate their floral resource use in an urban reserve. We collected three different pollen samples from hives: individual bees, raw honey and pollen traps, and identified plants using two metabarcoding markers (ITS2 and trnL). We then compared the results to a ground vegetation survey of surrounding flowering taxa. Pollen DNA metabarcoding detected 74 taxa (48.6% identified to species) across all pollen sources, compared to 44 taxa recorded by the survey (93% identified to species). Within the metabarcoding results, we identified 25% of the genera and 9% of the species found during the survey, with three of the top 10 flowering genera represented. While honey was the most taxon‐rich pollen source (mean = 8.5, SD = 3.5), followed by honey bees (mean = 5.8, SD = 6.1) and pollen traps (mean = 4.2, SD = 1.7), combining the results of six individual bees could detect similar taxa numbers to honey, while 20 bees were required to detect as many taxa as the survey. We demonstrate how DNA metabarcoding of the pollen foraged by honey bees can detect more flowering taxa than traditional survey methods, and how different pollen sources and genetic markers affect the level of detection of plant taxa. The foraging choices of honey bees matched few species detected by the vegetation survey, therefore pollen metabarcoding is recommended as a complementary approach to ground surveys. Rigorous validation and stringent filtering of metabarcoding results were also required to exclude potential false positives. Altogether, this molecular approach can be used to augment vegetation surveys, while tracking the floral resources used by bees.

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Environmental DNA as an emerging tool in botanical research

Johnson

Freeland

Parducci

et al. 2023

American J of Botany

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Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems. K E Y W O R D Sancient botanical eDNA, aquatic botanical eDNA, botanical eDNA, eDNA, organism derived botanical eDNA, review

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Rank‐based characterization of pollen assemblages collected by honey bees using a multi‐locus metabarcoding approach

Cited by 114 publications

References 29 publications

Pollen DNA barcoding: current applications and future prospects

Pollen DNA barcoding: current applications and future prospects

Monitoring of honey bee floral resources with pollen DNA metabarcoding as a complementary tool to vegetation surveys

Environmental DNA as an emerging tool in botanical research

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